1. Heat the oven to 425°F. Put the potatoes on a large baking sheet and toss with the olive oil. Sprinkle with 1 tsp. of the thyme, 1 tsp. salt, 1/2 tsp. pepper, and toss again. Bake the potatoes until they feel perfectly tender when pierced with a skewer, 20 to 25 minutes. Remove from the oven and let rest until cool enough to handle, about 10 minutes. If not working ahead, increase the oven temperature to 450°F.
2. Carefully hollow out each potato: Begin by slicing off the top; use a small spoon or a melon baller to scoop out most of the flesh inside, transferring it to a large bowl. Discard the tops. Mash the potato flesh with a masher or a fork, then combine it with the bacon, 1/4 cup of the chives, the sour cream, the remaining 1 tsp. thyme, 1/2 tsp. salt, and 1/4 tsp. pepper. Season to taste with more salt and pepper.
3. Using a small spoon, fill the hollowed potatoes with this mixture; it should mound a bit. Sprinkle on the cheese.
4. Return the potatoes to the 450°F oven and bake until the filling heats through, 8 to 10 minutes. Sprinkle with the remaining chives and serve warm.